Imputation accuracy for the 1000G, HRC and CONVERGE reference panels. (A) Imputation accuracy for the Han Chinese using four different reference panels. Only the mean EmpR² of low-frequency and rare variants were plotted, and the variants were divided into four MAF bins. The panel of ‘CHB + diversity (21%)’ was referred to the CHB21D panel, which consisted of CHB population and 21% extra diverse samples (i.e. the 3-step panel for Han Chinese in last section). (B) Imputation accuracy for the European population using three reference panels, and only three MAF bins of EmpR² of variants were plotted since the variants with MAF < 0.5% were not available (see Methods).